Structure of PDB 4ktc Chain A Binding Site BS03

Receptor Information

>4ktc Chain A (length=175) Species: 11116 (Hepatitis C virus (isolate Japanese))

APITAYSQQTRGLLGCIITSLTGRDKNQVDGEVQVLSTATQSFLATCVNG
VCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWPAPPGARSMTPCTCG
SSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHV
VGIFRAAVCTRGVAKAVDFIPVESM

Ligand information

• Ligand ID: 1X3
• InChI: InChI=1S/C37H51N5O9S/c43-32-31-20-28(51-36(47)41-19-18-24-10-6-7-11-25(24)22-41)23-42(31)33(44)30(38-35(46)50-27-13-8-9-14-27)15-5-3-1-2-4-12-26-21-37(26,39-32)34(45)40-52(48,49)29-16-17-29/h6-7,10-11,26-31H,1-5,8-9,12-23H2,(H,38,46)(H,39,43)(H,40,45)/t26-,28-,30+,31+,37-/m1/s1
• InChIKey: VQZYSHWAKCNHJX-IVYVMHIUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1ccc2c(c1)CCN(C2)C(=O)O[C@@H]3C[C@H]4C(=O)N[C@@]5(C[C@H]5CCCCCCC[C@@H](C(=O)N4C3)NC(=O)OC6CCCC6)C(=O)NS(=O)(=O)C7CC7
  OpenEye OEToolkits 1.7.6: c1ccc2c(c1)CCN(C2)C(=O)OC3CC4C(=O)NC5(CC5CCCCCCCC(C(=O)N4C3)NC(=O)OC6CCCC6)C(=O)NS(=O)(=O)C7CC7
  CACTVS 3.385: O=C(N[CH]1CCCCCCC[CH]2C[C]2(NC(=O)[CH]3C[CH](CN3C1=O)OC(=O)N4CCc5ccccc5C4)C(=O)N[S](=O)(=O)C6CC6)OC7CCCC7
  ACDLabs 12.01: O=S(=O)(NC(=O)C23NC(=O)C6N(C(=O)C(NC(=O)OC1CCCC1)CCCCCCCC3C2)CC(OC(=O)N5Cc4c(cccc4)CC5)C6)C7CC7
  CACTVS 3.385: O=C(N[C@H]1CCCCCCC[C@@H]2C[C@]2(NC(=O)[C@@H]3C[C@H](CN3C1=O)OC(=O)N4CCc5ccccc5C4)C(=O)N[S](=O)(=O)C6CC6)OC7CCCC7
• Formula: C37 H51 N5 O9 S
• ZINC: ZINC000098208045
• PDB chain: 4ktc Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ktc Discovery of Danoprevir (ITMN-191/R7227), a Highly Selective and Potent Inhibitor of Hepatitis C Virus (HCV) NS3/4A Protease.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): Q41 F43 H57 D81 V132 L135 K136 G137 S139 F154 R155 A156 A157 D168
• Binding residue (residue number reindexed from 1): Q41 F43 H57 D81 V132 L135 K136 G137 S139 F154 R155 A156 A157 D168
• Annotation score: 1
• Binding affinity: MOAD: ic50=1nM
  PDBbind-CN: -logKd/Ki=9.00,IC50=1nM

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D81 G137 S139
• Catalytic site (residue number reindexed from 1): H57 D81 G137 S139
• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.98: hepacivirin.
  3.4.22.-
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0008236 serine-type peptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0019087 transformation of host cell by virus

External links

• PDB: RCSB:4ktc, PDBe:4ktc, PDBj:4ktc
• PDBsum: 4ktc
• PubMed: 23672640
• UniProt: P26662|POLG_HCVJA Genome polyprotein